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Nucleic Acids Research Advance Access published online on November 4, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn746
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes

Ashwini Bhasi1, Philge Philip2, Vinu Manikandan2 and Periannan Senapathy1,2,*

1Department of Human Genetics, Genome International Corp, 8000 Excelsior Drive, Madison, WI 53717, USA and 2Department of Bioinformatics, International Center for Advanced Genomics and Proteomics, 83, 1st Cross Street, Nehru Nagar, Chennai 600096, India

*To whom correspondence should be addressed. Tel: (608) 239 6253; Fax: (608) 833 5856; Email: ps{at}genome.com

Received August 15, 2008. Revised October 2, 2008. Accepted October 3, 2008.

We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon–intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon–intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon–intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/.


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